Question: Design for introducing batch effect in DESeq2
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18 days ago by
ag1805x10
ag1805x10 wrote:

I have RNAseq data taken from two different ENA project IDs (PrjA & PrjB). Both PrjA & PrjB contains test and control samples. PrjA was PE 50bp sequencing while PrjB was SE 100bp. Is it possible we can combine the data to identify DEG between test and control? Would batch effect removal by Combat be a better option or use the design = project+condition in DESeq2?

modified 18 days ago by swbarnes2310 • written 18 days ago by ag1805x10

If you DO know the batches, then what swbarnes2 recommended is the best option. If you don't know then you could use sva.

In your case, however, I don't think that it's wise to just combine the data because it seems that you use different platforms for the sequencing. Could you show us the MDS plot?

Answer: Design for introducing batch effect in DESeq2
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18 days ago by
swbarnes2310
swbarnes2310 wrote:

Do what the DESeq software recommends. Give DESeq raw counts, not some kind of batch corrected, and include batch as a factor in the design.

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You can do that even when the data came from two different projects? Seems like the batch issue in this case is not simply multiple runs of the same instrument but other things are different as well.